Five protesters who broke into the boundary of the top secret military base at Pine Gap have been freed after a judge dropped charges because of "flawed" and "premature" police prosecution.

Key points:

Charges dismissed because police failed to gain Attorney-General's consent before prosecution began

Protesters campaigning to close down Pine Gap military base

Group are "faith-based activists" who "broke into base to pray and lament the war dead"

The protesters were arrested by Australian Federal Police early on Thursday after they breached the perimeter to the joint US-Australian defence facility outside Alice Springs.

The five were remanded in custody and have appeared in court in front of a large contingent of supporters, charged with Commonwealth offences.

The charges laid against the group were thrown out of court because the police failed to gain the consent of the Attorney-General before the prosecution began, as is the requirement in Commonwealth legislation.

Judge Daynor Trigg said the legislation was "a bit of nonsense" and "clearly didn't understand how the criminal justice system works" but the prosecution was "premature" and "flawed" and never should have proceeded.

However, Mr Trigg made it clear that the protesters could still be charged.

'Peace pilgrims' could face serious trespass charges

Protesters are this week campaigning to close down the military base, which has been in operation since 1970.

"They're so determined to get the evil of Pine Gap recognised that they went on there to pray and face serious charges of trespass on this secret base."

Meanwhile, four activists in Alice Springs chained themselves for several hours to the gates of a defence contractor supplying the Pine Gap base to block employees from getting to work.

"[We want to] let the workers know that there are people here who don't like what they're doing in working at a foreign military base outside Alice Springs, which is obviously responsible for [the] deaths of hundreds of people across the Middle East," said activist Jacob Grech, who chained his neck to a gate.

"We've successfully stopped the buses getting out ferrying the workers."

"There's no safety concerns for them at the moment, they're adults and they've made that choice to do that but we'll be talking to them about releasing themselves from that situation," Senior Sergeant Pauline Vickery said.

"However, when people start to impact on the common intercourse of other people's lives then obviously we have to intervene."

On Wednesday, dozens of people blockaded the access road into the base for more than two hours.

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